From: Albert (
Date: Sun Feb 12 2012 - 08:24:29 CST

   than you very much for kind messages.
   I am trying to extract DESMOND MD simulation files and I don't think
there would be any PSF/PDB file from Desmond output. It only contains
clickme.dtr and MD-out.cms files which I specified in the command:

catdcd -o mytest.pdb -otype pdb -i MD_trj/clickme.dtr -first 1 -last
2000 -s MD-out.cms

I DO type catdcd to get help from CATDCD for help but there is no more
comments for Desmond. So, I am turning to this maillist for helps.


On 02/12/2012 03:21 PM, JC Gumbart wrote:
> While –i for input may be intuitive, it’s actually used for an index
> file. Try typing just “catdcd” at the command line to see the correct
> way to use it. Note that you will also need to give it a PSF/PDB file
> as well.